I've heard other monks here say nice things about gnuplot.

Here is a perlmonks example: Plot a spiral with gnuplot.

This. If you want to make graphs for a scientific publication, use Gnuplot. Your other uppercase-f-Free options are Octave (who knows how it will turn out since they stopped using Gnuplot), some Python thing (SciPy, of which I know little), and doing it yourself by hand (learn PostScript or some other vector drawing language).

However, the linked node has a bunch of extraneous garbage. (Also, it doesn't even work, since it doesn't bother to flush the temporary file before using it.) All you really need is some version of:

open DATAFILE, ">$whatever";
# write data to DATAFILE
close DATAFILE;
open PLOT, "| gnuplot";
print PLOT <<EOS;
...
p '$whatever' ... (gnuplot options) ...
...
EOS
close PLOT;
[download]

Well don't use a temporary file then ;)

Just use gnuplot's special file '-' and inline the data.

I added a node to show how it's done to the above example at Re: Plot a spiral with gnuplot

However, the linked node has a bunch of extraneous garbage.

I don't see anything extraneous or any garbage. I found that node months ago when I was curious about gnuplot and found it to be short and sweet and to the point with helpful links.

(Also, it doesn't even work, since it doesn't bother to flush the temporary file before using it.)

It has been a while since I tried the code in that node but I just remember quickly having a plot of a pretty spiral without much (any) effort on my part.

use GD::Graph::points;

my $graph = GD::Graph::points->new;
$graph->set( 
        x_label     => 'Label', 
        y_label     => 'Values', 
        title          => 'Label By Value', 
        #cumulate     => 1, 
        dclrs         => [ 'black', 'black','black','black','black','b
+lack','black' ], 
        borderclrs     => [ qw(black black), qw(black black) ], 
        bar_spacing => 4, 
        transparent => 1,
        show_values => 1, 
); 

my $gd = $graph->plot(\@data) or die $graph->error; 

open(IMG, ">","$graph_file") or die $!;
binmode IMG;
print IMG $gd->gif;
close IMG;

[download]

You can take a look at chapter 5 of Graphics Programming with Perl as well as chapter 8 of Mastering Algorithms with Perl. The first will introduce you to GD::Graph, gnuplot and PGPLOT. The second is, as the title implies, a little more involved but provides further examples to try out.

PDL (Perl Data Language) comes with a command line interface and is supposed to be somewhat of a competitor to MATLAB. It may be a bit more than it seems like you're looking for but the documentation is really extensive and apparently includes (just from looking it over a few times) a thorough course.

Well, I have used gnuplot in the past, is correct and great but a little limited to my taste. You need to control and to specify all. Finally I get tired of if.

... on the other hand, R is awesome doing plots. You can call R from Perl easily.